SequenceComparison.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.


//////////////////////////////////////////////////////////////////////
/// @begin SequenceComparison
///
/// @brief
/// Compare the sequences between a native and designed protein
///
/// @detailed
/// This is an implementation taken from Ron Jacak, Douglas Renfrew, Matt O Mera.
/// The main function that is called is the get_sequence_recovery() function. You can
/// pass this function a list of native pdbs and designed pdbs, or just 1 native and 1
/// designed pdb. The sequence recovery will be output in a file called sequencerecovery.txt
/// along with a substitution matrix in a file called submatrix.txt
///
///
/// @references
/// "Native sequences are close to optimal" paper
///
///
/// @authors
/// Ron Jacak,
/// Douglas Renfrew (renfrew@unc.edu) ( added rotamer recovery, cleanup )
/// Steven Combs (moved it into a general use class)
///
/// @last_modified October 20 2010
/////////////////////////////////////////////////////////////////////////




#ifndef INCLUDED_protocols_toolbox_pose_metric_calculators_SequenceComparison_hh
#define INCLUDED_protocols_toolbox_pose_metric_calculators_SequenceComparison_hh

// AUTO-REMOVED #include <core/pose/Pose.hh>
#include <utility/vector1.hh>
// AUTO-REMOVED #include <core/pack/task/TaskFactory.hh>

// C++ headers
#include <set>

#include <core/types.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>



namespace protocols{
namespace toolbox{
namespace pose_metric_calculators{

class SequenceComparison{
public:
  //constructor to assign surface and core cutoff;
  SequenceComparison(core::Size surface, core::Size core) :
    surface_exposure_(surface),
    core_cutoff_(core)
  {

  }


  //default constructor
  SequenceComparison() :
    surface_exposure_(16),
    core_cutoff_(24)
  {

  }


  ///@brief main function that is called. calls measure_sequence_recovery
  void get_sequence_recovery(utility::vector1<core::pose::Pose> & native_poses, utility::vector1<core::pose::Pose> & redesign_poses);

  ///@brief overflowed main function to compare only two proteins
  void get_sequence_recovery(core::pose::Pose & native, core::pose::Pose & designed);

  ///@brief measures the sequence recovery of a list of native proteins and a list of designed proteins. Outputs files to sequencerecovery.txt
  void measure_sequence_recovery( utility::vector1<core::pose::Pose> & native_poses, utility::vector1<core::pose::Pose> & redesign_poses);
  void fill_num_neighbors( core::pose::Pose & pose, utility::vector1< core::Size > & num_nbs );

  ///@brief sets up the task factory used for determing what the neighbor counts...what is on the surface and what is in the core
  core::pack::task::TaskFactoryOP setup_tf( core::pack::task::TaskFactoryOP task_factory_ );
  std::set< core::Size > fill_designable_set( core::pose::Pose & pose, core::pack::task::TaskFactoryOP & tf );

private:

  ///@brief what is the surface cutoff that you are using? default 16
  core::Size surface_exposure_;

  ///@brief what is the core cutoff that you are using? default 24
  core::Size core_cutoff_;

};





}
}
}

#endif /* SEQUENCECOMPARISON_HH_ */